Biology has perennially been limited by the inability to generate complex cellular perturbations. Previous studies have screened for desired phenotypes using only single gene overexpression studies (Kitagawa et al. (2005) DNA Research 12:291-9; Soo et al. (2011) Proc Natl Acad Sci USA 108:1484-9) and single gene knockout studies, as well as a limited set of double-knockout studies (Butland et al. (2008) Nature Methods 5:789-95; Pan et al. (2004) Molecular Cell 16:487-96; Tong et al. (2004) Science 303:808-13). These methods, however, are not scalable to generating higher-order combinations of perturbations, preventing a more powerful and complex interrogation of networks. Furthermore, these methods are not easily scalable to generating more than a few thousand combinations. This prevents the screening and study of millions of combinations in a high-throughput pooled fashion, instead relying on well- or colony-based screening. Finally, these methods are not designed to enable rapid characterization of specific combinations.